Dissertation Defense: Zoe Malchiodi

Candidate: Zoe Malchiodi

Major: Tumor Biology

Advisor: Louis M. Weiner, M.D.

Title: Natural Killer Cells in the Pancreatic Ductal Adenocarcinoma Tumor Microenvironment

Pancreatic ductal adenocarcinoma (PDAC) is the most common form of pancreatic cancer. PDAC’s poor prognosis and resistance to chemo- and immunotherapies are attributed in part to its dense, fibrotic tumor microenvironment (TME), which is known to inhibit immune cell infiltration. Our laboratory recently determined that PDAC patients with higher natural killer (NK) cell content and activation have better survival rates. However, NK cell interactions in the PDAC TME have yet to be fully defined. Here, I used in vitro, in vivo, and multi-omics approaches to characterize NK cell interactions in the PDAC TME. I used spatial proteomics to assess NK cell content, spatial localization, and interactions in previously untreated human PDAC samples and found that active NK cells are present effector cells, both associate and interact with malignant epithelial cells, and that fibroblast-rich, desmoplastic epithelial-ductal regions limit NK cell infiltration in the PDAC TME. I then used single cell RNA sequencing (scRNA-seq) analysis, on a previously published human PDAC scRNA-seq dataset, to infer ligand-receptor (L-R) interactions and identified that the CD44 receptor on NK cells interacts with PDAC extracellular matrix (ECM) components such as collagens, fibronectin (FN1) and laminins expressed by fibroblasts and malignant epithelial cells. This led me to hypothesize that these interactions play roles in regulating NK cell motility in desmoplastic PDAC TMEs. Using 2D and 3D in vitro models, I found that CD44 neutralization significantly increased NK cell invasion through matrix. These findings demonstrate that NK cells are relevant in PDAC, and that targeting CD44-based or other receptors mediating ECM-immune cell interactions, such as LAIR-1, may increase NK cell invasion in the PDAC TME. Lastly, I used spatial transcriptomics to further contextualize gene signatures in CAF-high versus CAF-low epithelial-ductal regions and found that CAF-high epithelial-ductal regions are highly enriched for genes associated with epithelial-to-mesenchymal transition. These findings highlight the heterogeneity of the PDAC TME where further characterization of NK cell interactions in PDAC may identify additional potential therapeutic targets to increase NK cell-mediated anti-tumor immune responses.